187 results on '"Stein Aerts"'
Search Results
2. Shared enhancer gene regulatory networks between wound and oncogenic programs
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Swann Floc'hlay, Ramya Balaji, Dimitrije Stanković, Valerie M Christiaens, Carmen Bravo González-Blas, Seppe De Winter, Gert J Hulselmans, Maxime De Waegeneer, Xiaojiang Quan, Duygu Koldere, Mardelle Atkins, Georg Halder, Mirka Uhlirova, Anne-Kathrin Classen, and Stein Aerts
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wound response ,enhancer ,cancer ,gene regulatory network ,chromatin accessibility ,single-cell multiomics ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Wound response programs are often activated during neoplastic growth in tumors. In both wound repair and tumor growth, cells respond to acute stress and balance the activation of multiple programs, including apoptosis, proliferation, and cell migration. Central to those responses are the activation of the JNK/MAPK and JAK/STAT signaling pathways. Yet, to what extent these signaling cascades interact at the cis-regulatory level and how they orchestrate different regulatory and phenotypic responses is still unclear. Here, we aim to characterize the regulatory states that emerge and cooperate in the wound response, using the Drosophila melanogaster wing disc as a model system, and compare these with cancer cell states induced by rasV12scrib-/- in the eye disc. We used single-cell multiome profiling to derive enhancer gene regulatory networks (eGRNs) by integrating chromatin accessibility and gene expression signals. We identify a ‘proliferative’ eGRN, active in the majority of wounded cells and controlled by AP-1 and STAT. In a smaller, but distinct population of wound cells, a ‘senescent’ eGRN is activated and driven by C/EBP-like transcription factors (Irbp18, Xrp1, Slow border, and Vrille) and Scalloped. These two eGRN signatures are found to be active in tumor cells at both gene expression and chromatin accessibility levels. Our single-cell multiome and eGRNs resource offers an in-depth characterization of the senescence markers, together with a new perspective on the shared gene regulatory programs acting during wound response and oncogenesis.
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- 2023
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3. Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq
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Viacheslav Mylka, Irina Matetovici, Suresh Poovathingal, Jeroen Aerts, Niels Vandamme, Ruth Seurinck, Kevin Verstaen, Gert Hulselmans, Silvie Van den Hoecke, Isabelle Scheyltjens, Kiavash Movahedi, Hans Wils, Joke Reumers, Jeroen Van Houdt, Stein Aerts, and Yvan Saeys
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Hashing ,scRNA-seq ,MULTI-seq ,CITE-seq ,Sample multiplexing ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background Multiplexing of samples in single-cell RNA-seq studies allows a significant reduction of the experimental costs, straightforward identification of doublets, increased cell throughput, and reduction of sample-specific batch effects. Recently published multiplexing techniques using oligo-conjugated antibodies or -lipids allow barcoding sample-specific cells, a process called “hashing.” Results Here, we compare the hashing performance of TotalSeq-A and -C antibodies, custom synthesized lipids and MULTI-seq lipid hashes in four cell lines, both for single-cell RNA-seq and single-nucleus RNA-seq. We also compare TotalSeq-B antibodies with CellPlex reagents (10x Genomics) on human PBMCs and TotalSeq-B with different lipids on primary mouse tissues. Hashing efficiency was evaluated using the intrinsic genetic variation of the cell lines and mouse strains. Antibody hashing was further evaluated on clinical samples using PBMCs from healthy and SARS-CoV-2 infected patients, where we demonstrate a more affordable approach for large single-cell sequencing clinical studies, while simultaneously reducing batch effects. Conclusions Benchmarking of different hashing strategies and computational pipelines indicates that correct demultiplexing can be achieved with both lipid- and antibody-hashed human cells and nuclei, with MULTISeqDemux as the preferred demultiplexing function and antibody-based hashing as the most efficient protocol on cells. On nuclei datasets, lipid hashing delivers the best results. Lipid hashing also outperforms antibodies on cells isolated from mouse brain. However, antibodies demonstrate better results on tissues like spleen or lung.
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- 2022
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4. Actuation enhances patterning in human neural tube organoids
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Abdel Rahman Abdel Fattah, Brian Daza, Gregorius Rustandi, Miguel Ángel Berrocal-Rubio, Benjamin Gorissen, Suresh Poovathingal, Kristofer Davie, Jorge Barrasa-Fano, Mar Cóndor, Xuanye Cao, Derek Hadar Rosenzweig, Yunping Lei, Richard Finnell, Catherine Verfaillie, Maurilio Sampaolesi, Peter Dedecker, Hans Van Oosterwyck, Stein Aerts, and Adrian Ranga
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Science - Abstract
Mechanical forces, along with gene regulatory networks and cell-cell signalling, play an important role in the complex organization of tissues. Here the authors describe devices that actively apply mechanical force to developing neural tube, demonstrating that mechanical forces increase growth and enhance patterning.
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- 2021
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5. Reduced Levels of Misfolded and Aggregated Mutant p53 by Proteostatic Activation
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Evelyne Naus, Marleen Derweduwe, Youlia Lampi, Annelies Claeys, Jarne Pauwels, Tobias Langenberg, Filip Claes, Jie Xu, Veerle Haemels, Zeynep Kalender Atak, Rob van der Kant, Joost Van Durme, Greet De Baets, Keith L. Ligon, Mark Fiers, Kris Gevaert, Stein Aerts, Frederic Rousseau, Joost Schymkowitz, and Frederik De Smet
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protein aggregation ,p53 ,heat-shock ,proteostasic modulation ,Cytology ,QH573-671 - Abstract
In malignant cancer, excessive amounts of mutant p53 often lead to its aggregation, a feature that was recently identified as druggable. Here, we describe that induction of a heat shock-related stress response mediated by Foldlin, a small-molecule tool compound, reduces the protein levels of misfolded/aggregated mutant p53, while contact mutants or wild-type p53 remain largely unaffected. Foldlin also prevented the formation of stress-induced p53 nuclear inclusion bodies. Despite our inability to identify a specific molecular target, Foldlin also reduced protein levels of aggregating SOD1 variants. Finally, by screening a library of 778 FDA-approved compounds for their ability to reduce misfolded mutant p53, we identified the proteasome inhibitor Bortezomib with similar cellular effects as Foldlin. Overall, the induction of a cellular heat shock response seems to be an effective strategy to deal with pathological protein aggregation. It remains to be seen however, how this strategy can be translated to a clinical setting.
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- 2023
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6. Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads
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Florian V De Rop, Joy N Ismail, Carmen Bravo González-Blas, Gert J Hulselmans, Christopher Campbell Flerin, Jasper Janssens, Koen Theunis, Valerie M Christiaens, Jasper Wouters, Gabriele Marcassa, Joris de Wit, Suresh Poovathingal, and Stein Aerts
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single-cell RNA sequencing ,single-cell ATAC sequencing ,scRNA-seq ,scATAC-seq ,droplet microfluidics ,hydrop ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Single-cell RNA-seq and single-cell assay for transposase-accessible chromatin (ATAC-seq) technologies are used extensively to create cell type atlases for a wide range of organisms, tissues, and disease processes. To increase the scale of these atlases, lower the cost and pave the way for more specialized multiome assays, custom droplet microfluidics may provide solutions complementary to commercial setups. We developed HyDrop, a flexible and open-source droplet microfluidic platform encompassing three protocols. The first protocol involves creating dissolvable hydrogel beads with custom oligos that can be released in the droplets. In the second protocol, we demonstrate the use of these beads for HyDrop-ATAC, a low-cost noncommercial scATAC-seq protocol in droplets. After validating HyDrop-ATAC, we applied it to flash-frozen mouse cortex and generated 7996 high-quality single-cell chromatin accessibility profiles in a single run. In the third protocol, we adapt both the reaction chemistry and the capture sequence of the barcoded hydrogel bead to capture mRNA, and demonstrate a significant improvement in throughput and sensitivity compared to previous open-source droplet-based scRNA-seq assays (Drop-seq and inDrop). Similarly, we applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes closely matching reference single-cell gene expression data. Finally, we leveraged HyDrop-RNA’s high capture rate to analyze a small population of fluorescence-activated cell sorted neurons from the Drosophila brain, confirming the protocol’s applicability to low input samples and small cells. HyDrop is currently capable of generating single-cell data in high throughput and at a reduced cost compared to commercial methods, and we envision that HyDrop can be further developed to be compatible with novel (multi) omics protocols.
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- 2022
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7. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings
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Isabel Almudi, Joel Vizueta, Christopher D. R. Wyatt, Alex de Mendoza, Ferdinand Marlétaz, Panos N. Firbas, Roberto Feuda, Giulio Masiero, Patricia Medina, Ana Alcaina-Caro, Fernando Cruz, Jessica Gómez-Garrido, Marta Gut, Tyler S. Alioto, Carlos Vargas-Chavez, Kristofer Davie, Bernhard Misof, Josefa González, Stein Aerts, Ryan Lister, Jordi Paps, Julio Rozas, Alejandro Sánchez-Gracia, Manuel Irimia, Ignacio Maeso, and Fernando Casares
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Science - Abstract
Genomic studies of paleopteran insects, such as mayflies, are needed to reconstruct early insect evolution. Here, Almudi and colleagues present the genome of the mayfly Cloeon dipterum and use transcriptomics to characterize its adaptations to distinct habitats and the origin of insect wings.
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- 2020
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8. Analysis of long and short enhancers in melanoma cell states
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David Mauduit, Ibrahim Ihsan Taskiran, Liesbeth Minnoye, Maxime de Waegeneer, Valerie Christiaens, Gert Hulselmans, Jonas Demeulemeester, Jasper Wouters, and Stein Aerts
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melanoma ,enhancers ,MPRA ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Understanding how enhancers drive cell-type specificity and efficiently identifying them is essential for the development of innovative therapeutic strategies. In melanoma, the melanocytic (MEL) and the mesenchymal-like (MES) states present themselves with different responses to therapy, making the identification of specific enhancers highly relevant. Using massively parallel reporter assays (MPRAs) in a panel of patient-derived melanoma lines (MM lines), we set to identify and decipher melanoma enhancers by first focusing on regions with state-specific H3K27 acetylation close to differentially expressed genes. An in-depth evaluation of those regions was then pursued by investigating the activity of overlapping ATAC-seq peaks along with a full tiling of the acetylated regions with 190 bp sequences. Activity was observed in more than 60% of the selected regions, and we were able to precisely locate the active enhancers within ATAC-seq peaks. Comparison of sequence content with activity, using the deep learning model DeepMEL2, revealed that AP-1 alone is responsible for the MES enhancer activity. In contrast, SOX10 and MITF both influence MEL enhancer function with SOX10 being required to achieve high levels of activity. Overall, our MPRAs shed light on the relationship between long and short sequences in terms of their sequence content, enhancer activity, and specificity across melanoma cell states.
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- 2021
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9. Tyrosine-Dependent Phenotype Switching Occurs Early in Many Primary Melanoma Cultures Limiting Their Translational Value
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Ahmad Najem, Jasper Wouters, Mohammad Krayem, Florian Rambow, Malak Sabbah, François Sales, Ahmad Awada, Stein Aerts, Fabrice Journe, Jean-Christophe Marine, and Ghanem E. Ghanem
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melanoma ,primary cultures ,phenotype switching ,tyrosine ,pigmentation ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
The use of patient-derived primary cell cultures in cancer preclinical assays, including drug screens and genotoxic studies, has increased in recent years. However, their translational value is constrained by several limitations, including variability that can be caused by the culture conditions. Here, we show that the medium composition commonly used to propagate primary melanoma cultures has limited their representability of their tumor of origin and their cellular plasticity, and modified their sensitivity to therapy. Indeed, we established and compared cultures from different melanoma patients propagated in parallel in low-tyrosine (Ham’s F10) or in high-tyrosine (Ham’s F10 supplemented with tyrosine or RPMI1640 or DMEM) media. Tyrosine is the precursor of melanin biosynthesis, a process particularly active in differentiated melanocytes and melanoma cells. Unexpectedly, we found that the high tyrosine concentrations promoted an early phenotypic drift towards either a mesenchymal-like or senescence-like phenotype, and prevented the establishment of cultures of melanoma cells harboring differentiated features, which we show are frequently present in human clinical biopsies. Moreover, the invasive phenotype emerging in these culture conditions appeared irreversible and, as expected, associated with intrinsic resistance to MAPKi. In sharp contrast, differentiated melanoma cell cultures retained their phenotypes upon propagation in low-tyrosine medium, and importantly their phenotypic plasticity, a key hallmark of melanoma cells. Altogether, our findings underline the importance of culturing melanoma cells in low-tyrosine-containing medium in order to preserve their phenotypic identity of origin and cellular plasticity.
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- 2021
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10. Establishment of the mayfly Cloeon dipterum as a new model system to investigate insect evolution
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Isabel Almudi, Carlos A. Martín-Blanco, Isabel M. García-Fernandez, Adrián López-Catalina, Kristofer Davie, Stein Aerts, and Fernando Casares
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Evolutionary and developmental biology ,Insect evolution ,Embryogenesis ,Paleoptera ,Mayflies ,Ephemeroptera ,Evolution ,QH359-425 - Abstract
Abstract The great capability of insects to adapt to new environments promoted their extraordinary diversification, resulting in the group of Metazoa with the largest number of species distributed worldwide. To understand this enormous diversity, it is essential to investigate lineages that would allow the reconstruction of the early events in the evolution of insects. However, research on insect ecology, physiology, development and evolution has mostly focused on few well-established model species. The key phylogenetic position of mayflies within Paleoptera as the sister group of the rest of winged insects and life history traits of mayflies make them an essential order to understand insect evolution. Here, we describe the establishment of a continuous culture system of the mayfly Cloeon dipterum and a series of experimental protocols and omics resources that allow the study of its development and its great regenerative capability. Thus, the establishment of Cloeon as an experimental platform paves the way to understand genomic and morphogenetic events that occurred at the origin of winged insects.
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- 2019
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11. Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
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Carmen Bravo González‐Blas, Xiao‐Jiang Quan, Ramon Duran‐Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime deWaegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, and Stein Aerts
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enhancer detection ,eye‐antennal disc ,gene regulation ,single‐cell omics ,spatial integration ,Biology (General) ,QH301-705.5 ,Medicine (General) ,R5-920 - Abstract
Abstract Single‐cell technologies allow measuring chromatin accessibility and gene expression in each cell, but jointly utilizing both layers to map bona fide gene regulatory networks and enhancers remains challenging. Here, we generate independent single‐cell RNA‐seq and single‐cell ATAC‐seq atlases of the Drosophila eye‐antennal disc and spatially integrate the data into a virtual latent space that mimics the organization of the 2D tissue using ScoMAP (Single‐Cell Omics Mapping into spatial Axes using Pseudotime ordering). To validate spatially predicted enhancers, we use a large collection of enhancer–reporter lines and identify ~ 85% of enhancers in which chromatin accessibility and enhancer activity are coupled. Next, we infer enhancer‐to‐gene relationships in the virtual space, finding that genes are mostly regulated by multiple, often redundant, enhancers. Exploiting cell type‐specific enhancers, we deconvolute cell type‐specific effects of bulk‐derived chromatin accessibility QTLs. Finally, we discover that Prospero drives neuronal differentiation through the binding of a GGG motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue.
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- 2020
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12. Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks
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Zeynep Kalender Atak, Hana Imrichova, Dmitry Svetlichnyy, Gert Hulselmans, Valerie Christiaens, Joke Reumers, Hugo Ceulemans, and Stein Aerts
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cis-regulatory mutations ,Whole-genome sequencing ,Gene regulatory networks ,Cancer genomics ,Medicine ,Genetics ,QH426-470 - Abstract
Abstract The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying “personal” gene regulatory network. We validated μ-cisTarget by re-analyzing the TAL1 and LMO1 enhancer mutations in T-ALL, and the TERT promoter mutation in melanoma. Next, we re-sequenced the full genomes of ten cancer cell lines and used matched transcriptome data and motif discovery to identify master regulators with de novo binding sites that result in the up-regulation of nearby oncogenic drivers. μ-cisTarget is available from http://mucistarget.aertslab.org .
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- 2017
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13. Nuclear receptors connect progenitor transcription factors to cell cycle control
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Marta Neto, Marina Naval-Sánchez, Delphine Potier, Paulo S. Pereira, Dirk Geerts, Stein Aerts, and Fernando Casares
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Medicine ,Science - Abstract
Abstract The specification and growth of organs is controlled simultaneously by networks of transcription factors. While the connection between these transcription factors with fate determinants is increasingly clear, how they establish the link with the cell cycle is far less understood. Here we investigate this link in the developing Drosophila eye, where two transcription factors, the MEIS1 homologue hth and the Zn-finger tsh, synergize to stimulate the proliferation of naïve eye progenitors. Experiments combining transcriptomics, open-chromatin profiling, motif analysis and functional assays indicate that these progenitor transcription factors exert a global regulation of the proliferation program. Rather than directly regulating cell cycle genes, they control proliferation through an intermediary layer of nuclear receptors of the ecdysone/estrogen-signaling pathway. This regulatory subnetwork between hth, tsh and nuclear receptors might be conserved from Drosophila to mammals, as we find a significant co-overexpression of their human homologues in specific cancer types.
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- 2017
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14. A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing
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Karen Verboom, Wouter Van Loocke, Pieter-Jan Volders, Bieke Decaesteker, Francisco Avila Cobos, Simon Bornschein, Charles E. de Bock, Zeynep Kalender Atak, Emmanuelle Clappier, Stein Aerts, Jan Cools, Jean Soulier, Tom Taghon, Pieter Van Vlierberghe, Jo Vandesompele, Frank Speleman, and Kaat Durinck
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Diseases of the blood and blood-forming organs ,RC633-647.5 - Published
- 2018
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15. Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference
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Delphine Potier, Kristofer Davie, Gert Hulselmans, Marina Naval Sanchez, Lotte Haagen, Vân Anh Huynh-Thu, Duygu Koldere, Arzu Celik, Pierre Geurts, Valerie Christiaens, and Stein Aerts
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Biology (General) ,QH301-705.5 - Abstract
Genome control is operated by transcription factors (TFs) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRNs). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse engineer the GRNs of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types and inferred a coexpression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5,632 direct target genes through 24,926 enhancers. Using this network, we found network motifs, cis-regulatory codes, and regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general cofactor in the eye network, being bound to thousands of nucleosome-free regions.
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- 2014
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16. TDP-43 Loss-of-Function Causes Neuronal Loss Due to Defective Steroid Receptor-Mediated Gene Program Switching in Drosophila
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Lies Vanden Broeck, Marina Naval-Sánchez, Yoshitsugu Adachi, Danielle Diaper, Pierre Dourlen, Julien Chapuis, Gernot Kleinberger, Marc Gistelinck, Christine Van Broeckhoven, Jean-Charles Lambert, Frank Hirth, Stein Aerts, Patrick Callaerts, and Bart Dermaut
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Biology (General) ,QH301-705.5 - Abstract
TDP-43 proteinopathy is strongly implicated in the pathogenesis of amyotrophic lateral sclerosis and related neurodegenerative disorders. Whether TDP-43 neurotoxicity is caused by a novel toxic gain-of-function mechanism of the aggregates or by a loss of its normal function is unknown. We increased and decreased expression of TDP-43 (dTDP-43) in Drosophila. Although upregulation of dTDP-43 induced neuronal ubiquitin and dTDP-43-positive inclusions, both up- and downregulated dTDP-43 resulted in selective apoptosis of bursicon neurons and highly similar transcriptome alterations at the pupal-adult transition. Gene network analysis and genetic validation showed that both up- and downregulated dTDP-43 directly and dramatically increased the expression of the neuronal microtubule-associated protein Map205, resulting in cytoplasmic accumulations of the ecdysteroid receptor (EcR) and a failure to switch EcR-dependent gene programs from a pupal to adult pattern. We propose that dTDP-43 neurotoxicity is caused by a loss of its normal function.
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- 2013
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17. dachshund Potentiates Hedgehog Signaling during Drosophila Retinogenesis.
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Catarina Brás-Pereira, Delphine Potier, Jelle Jacobs, Stein Aerts, Fernando Casares, and Florence Janody
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Genetics ,QH426-470 - Abstract
Proper organ patterning depends on a tight coordination between cell proliferation and differentiation. The patterning of Drosophila retina occurs both very fast and with high precision. This process is driven by the dynamic changes in signaling activity of the conserved Hedgehog (Hh) pathway, which coordinates cell fate determination, cell cycle and tissue morphogenesis. Here we show that during Drosophila retinogenesis, the retinal determination gene dachshund (dac) is not only a target of the Hh signaling pathway, but is also a modulator of its activity. Using developmental genetics techniques, we demonstrate that dac enhances Hh signaling by promoting the accumulation of the Gli transcription factor Cubitus interruptus (Ci) parallel to or downstream of fused. In the absence of dac, all Hh-mediated events associated to the morphogenetic furrow are delayed. One of the consequences is that, posterior to the furrow, dac- cells cannot activate a Roadkill-Cullin3 negative feedback loop that attenuates Hh signaling and which is necessary for retinal cells to continue normal differentiation. Therefore, dac is part of an essential positive feedback loop in the Hh pathway, guaranteeing the speed and the accuracy of Drosophila retinogenesis.
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- 2016
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18. Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models.
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Dmitry Svetlichnyy, Hana Imrichova, Mark Fiers, Zeynep Kalender Atak, and Stein Aerts
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Biology (General) ,QH301-705.5 - Abstract
Cancer genomes contain vast amounts of somatic mutations, many of which are passenger mutations not involved in oncogenesis. Whereas driver mutations in protein-coding genes can be distinguished from passenger mutations based on their recurrence, non-coding mutations are usually not recurrent at the same position. Therefore, it is still unclear how to identify cis-regulatory driver mutations, particularly when chromatin data from the same patient is not available, thus relying only on sequence and expression information. Here we use machine-learning methods to predict functional regulatory regions using sequence information alone, and compare the predicted activity of the mutated region with the reference sequence. This way we define the Predicted Regulatory Impact of a Mutation in an Enhancer (PRIME). We find that the recently identified driver mutation in the TAL1 enhancer has a high PRIME score, representing a "gain-of-target" for MYB, whereas the highly recurrent TERT promoter mutation has a surprisingly low PRIME score. We trained Random Forest models for 45 cancer-related transcription factors, and used these to score variations in the HeLa genome and somatic mutations across more than five hundred cancer genomes. Each model predicts only a small fraction of non-coding mutations with a potential impact on the function of the encompassing regulatory region. Nevertheless, as these few candidate driver mutations are often linked to gains in chromatin activity and gene expression, they may contribute to the oncogenic program by altering the expression levels of specific oncogenes and tumor suppressor genes.
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- 2015
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19. Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells
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Patrick Laurette, Thomas Strub, Dana Koludrovic, Céline Keime, Stéphanie Le Gras, Hannah Seberg, Eric Van Otterloo, Hana Imrichova, Robert Siddaway, Stein Aerts, Robert A Cornell, Gabrielle Mengus, and Irwin Davidson
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chromatin remodelling ,SOX10 ,CHD7 ,YY1 ,TFAP2A ,enhancer ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Microphthalmia-associated transcription factor (MITF) is the master regulator of the melanocyte lineage. To understand how MITF regulates transcription, we used tandem affinity purification and mass spectrometry to define a comprehensive MITF interactome identifying novel cofactors involved in transcription, DNA replication and repair, and chromatin organisation. We show that MITF interacts with a PBAF chromatin remodelling complex comprising BRG1 and CHD7. BRG1 is essential for melanoma cell proliferation in vitro and for normal melanocyte development in vivo. MITF and SOX10 actively recruit BRG1 to a set of MITF-associated regulatory elements (MAREs) at active enhancers. Combinations of MITF, SOX10, TFAP2A, and YY1 bind between two BRG1-occupied nucleosomes thus defining both a signature of transcription factors essential for the melanocyte lineage and a specific chromatin organisation of the regulatory elements they occupy. BRG1 also regulates the dynamics of MITF genomic occupancy. MITF-BRG1 interplay thus plays an essential role in transcription regulation in melanoma.
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- 2015
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20. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling.
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Kristofer Davie, Jelle Jacobs, Mardelle Atkins, Delphine Potier, Valerie Christiaens, Georg Halder, and Stein Aerts
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Genetics ,QH426-470 - Abstract
Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes.
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- 2015
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21. Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks
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Hui Zhao, Bernard Thienpont, Betül Tuba Yesilyurt, Matthieu Moisse, Joke Reumers, Lieve Coenegrachts, Xavier Sagaert, Stefanie Schrauwen, Dominiek Smeets, Gert Matthijs, Stein Aerts, Jan Cools, Alex Metcalf, Amanda Spurdle, ANECS, Frederic Amant, and Diether Lambrechts
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whole-genome sequencing ,mismatch repair deficiency ,mutation pattern ,MSI ,DNA double-strand break ,DSB inducer ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
DNA replication errors that persist as mismatch mutations make up the molecular fingerprint of mismatch repair (MMR)-deficient tumors and convey them with resistance to standard therapy. Using whole-genome and whole-exome sequencing, we here confirm an MMR-deficient mutation signature that is distinct from other tumor genomes, but surprisingly similar to germ-line DNA, indicating that a substantial fraction of human genetic variation arises through mutations escaping MMR. Moreover, we identify a large set of recurrent indels that may serve to detect microsatellite instability (MSI). Indeed, using endometrial tumors with immunohistochemically proven MMR deficiency, we optimize a novel marker set capable of detecting MSI and show it to have greater specificity and selectivity than standard MSI tests. Additionally, we show that recurrent indels are enriched for the ‘DNA double-strand break repair by homologous recombination’ pathway. Consequently, DSB repair is reduced in MMR-deficient tumors, triggering a dose-dependent sensitivity of MMR-deficient tumor cultures to DSB inducers.
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- 2014
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22. iRegulon: from a gene list to a gene regulatory network using large motif and track collections.
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Rekin's Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval Sanchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean-Christophe Marine, and Stein Aerts
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Identifying master regulators of biological processes and mapping their downstream gene networks are key challenges in systems biology. We developed a computational method, called iRegulon, to reverse-engineer the transcriptional regulatory network underlying a co-expressed gene set using cis-regulatory sequence analysis. iRegulon implements a genome-wide ranking-and-recovery approach to detect enriched transcription factor motifs and their optimal sets of direct targets. We increase the accuracy of network inference by using very large motif collections of up to ten thousand position weight matrices collected from various species, and linking these to candidate human TFs via a motif2TF procedure. We validate iRegulon on gene sets derived from ENCODE ChIP-seq data with increasing levels of noise, and we compare iRegulon with existing motif discovery methods. Next, we use iRegulon on more challenging types of gene lists, including microRNA target sets, protein-protein interaction networks, and genetic perturbation data. In particular, we over-activate p53 in breast cancer cells, followed by RNA-seq and ChIP-seq, and could identify an extensive up-regulated network controlled directly by p53. Similarly we map a repressive network with no indication of direct p53 regulation but rather an indirect effect via E2F and NFY. Finally, we generalize our computational framework to include regulatory tracks such as ChIP-seq data and show how motif and track discovery can be combined to map functional regulatory interactions among co-expressed genes. iRegulon is available as a Cytoscape plugin from http://iregulon.aertslab.org.
- Published
- 2014
- Full Text
- View/download PDF
23. Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia.
- Author
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Zeynep Kalender Atak, Valentina Gianfelici, Gert Hulselmans, Kim De Keersmaecker, Arun George Devasia, Ellen Geerdens, Nicole Mentens, Sabina Chiaretti, Kaat Durinck, Anne Uyttebroeck, Peter Vandenberghe, Iwona Wlodarska, Jacqueline Cloos, Robin Foà, Frank Speleman, Jan Cools, and Stein Aerts
- Subjects
Genetics ,QH426-470 - Abstract
RNA-seq is a promising technology to re-sequence protein coding genes for the identification of single nucleotide variants (SNV), while simultaneously obtaining information on structural variations and gene expression perturbations. We asked whether RNA-seq is suitable for the detection of driver mutations in T-cell acute lymphoblastic leukemia (T-ALL). These leukemias are caused by a combination of gene fusions, over-expression of transcription factors and cooperative point mutations in oncogenes and tumor suppressor genes. We analyzed 31 T-ALL patient samples and 18 T-ALL cell lines by high-coverage paired-end RNA-seq. First, we optimized the detection of SNVs in RNA-seq data by comparing the results with exome re-sequencing data. We identified known driver genes with recurrent protein altering variations, as well as several new candidates including H3F3A, PTK2B, and STAT5B. Next, we determined accurate gene expression levels from the RNA-seq data through normalizations and batch effect removal, and used these to classify patients into T-ALL subtypes. Finally, we detected gene fusions, of which several can explain the over-expression of key driver genes such as TLX1, PLAG1, LMO1, or NKX2-1; and others result in novel fusion transcripts encoding activated kinases (SSBP2-FER and TPM3-JAK2) or involving MLLT10. In conclusion, we present novel analysis pipelines for variant calling, variant filtering, and expression normalization on RNA-seq data, and successfully applied these for the detection of translocations, point mutations, INDELs, exon-skipping events, and expression perturbations in T-ALL.
- Published
- 2013
- Full Text
- View/download PDF
24. High accuracy mutation detection in leukemia on a selected panel of cancer genes.
- Author
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Zeynep Kalender Atak, Kim De Keersmaecker, Valentina Gianfelici, Ellen Geerdens, Roel Vandepoel, Daphnie Pauwels, Michaël Porcu, Idoya Lahortiga, Vanessa Brys, Willy G Dirks, Hilmar Quentmeier, Jacqueline Cloos, Harry Cuppens, Anne Uyttebroeck, Peter Vandenberghe, Jan Cools, and Stein Aerts
- Subjects
Medicine ,Science - Abstract
With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted mutations with a large independent validation set obtained by capillary re-sequencing. We found that the combination of two mapping algorithms, namely BWA-SW and SSAHA2, coupled with the variant calling algorithm Atlas-SNP2 yields the highest sensitivity (95%) and the highest specificity (93%). Next, we applied this analysis pipeline to identify mutations in a set of 58 cancer genes, in a panel of 18 T-ALL cell lines and 15 T-ALL patient samples. We confirmed mutations in known T-ALL drivers, including PHF6, NF1, FBXW7, NOTCH1, KRAS, NRAS, PIK3CA, and PTEN. Interestingly, we also found mutations in several cancer genes that had not been linked to T-ALL before, including JAK3. Finally, we re-sequenced a small set of 39 candidate genes and identified recurrent mutations in TET1, SPRY3 and SPRY4. In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations.
- Published
- 2012
- Full Text
- View/download PDF
25. Mutation analysis of the tyrosine phosphatase PTPN2 in Hodgkin’s lymphoma and T-cell non-Hodgkin’s lymphoma
- Author
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Maria Kleppe, Thomas Tousseyn, Eva Geissinger, Zeynep Kalender Atak, Stein Aerts, Andreas Rosenwald, Iwona Wlodarska, and Jan Cools
- Subjects
Diseases of the blood and blood-forming organs ,RC633-647.5 - Abstract
We recently reported deletion of the protein tyrosine phosphatase gene PTPN2 in T-cell acute lymphoblastic leukemia. Functional analyses confirmed that PTPN2 acts as classical tumor suppressor repressing the proliferation of T cells, in part through inhibition of JAK/STAT signaling. We investigated the expression of PTPN2 in leukemia as well as lymphoma cell lines. We identified bi-allelic inactivation of PTPN2 in the Hodgkin’s lymphoma cell line SUP-HD1 which was associated with activation of the JAK/STAT pathway. Subsequent sequence analysis of Hodgkin’s lymphoma and T-cell non-Hodgkin’s lymphoma identified bi-allelic inactivation of PTPN2 in 2 out of 39 cases of peripheral T-cell lymphoma not otherwise specified, but not in Hodgkin’s lymphoma. These results, together with our own data on T-cell acute lymphoblastic leukemia, demonstrate that PTPN2 is a tumor suppressor gene in T-cell malignancies.
- Published
- 2011
- Full Text
- View/download PDF
26. Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification.
- Author
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Stein Aerts, Xiao-Jiang Quan, Annelies Claeys, Marina Naval Sanchez, Phillip Tate, Jiekun Yan, and Bassem A Hassan
- Subjects
Biology (General) ,QH301-705.5 - Abstract
A comprehensive systems-level understanding of developmental programs requires the mapping of the underlying gene regulatory networks. While significant progress has been made in mapping a few such networks, almost all gene regulatory networks underlying cell-fate specification remain unknown and their discovery is significantly hampered by the paucity of generalized, in vivo validated tools of target gene and functional enhancer discovery. We combined genetic transcriptome perturbations and comprehensive computational analyses to identify a large cohort of target genes of the proneural and tumor suppressor factor Atonal, which specifies the switch from undifferentiated pluripotent cells to R8 photoreceptor neurons during larval development. Extensive in vivo validations of the predicted targets for the proneural factor Atonal demonstrate a 50% success rate of bona fide targets. Furthermore we show that these enhancers are functionally conserved by cloning orthologous enhancers from Drosophila ananassae and D. virilis in D. melanogaster. Finally, to investigate cis-regulatory cross-talk between Ato and other retinal differentiation transcription factors (TFs), we performed motif analyses and independent target predictions for Eyeless, Senseless, Suppressor of Hairless, Rough, and Glass. Our analyses show that cisTargetX identifies the correct motif from a set of coexpressed genes and accurately predicts target genes of individual TFs. The validated set of novel Ato targets exhibit functional enrichment of signaling molecules and a subset is predicted to be coregulated by other TFs within the retinal gene regulatory network.
- Published
- 2010
- Full Text
- View/download PDF
27. The atonal proneural transcription factor links differentiation and tumor formation in Drosophila.
- Author
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Wouter Bossuyt, Natalie De Geest, Stein Aerts, Iris Leenaerts, Peter Marynen, and Bassem A Hassan
- Subjects
Biology (General) ,QH301-705.5 - Abstract
The acquisition of terminal cell fate and onset of differentiation are instructed by cell type-specific master control genes. Loss of differentiation is frequently observed during cancer progression, but the underlying causes and mechanisms remain poorly understood. We tested the hypothesis that master regulators of differentiation may be key regulators of tumor formation. Using loss- and gain-of-function analyses in Drosophila, we describe a critical anti-oncogenic function for the atonal transcription factor in the fly retina, where atonal instructs tissue differentiation. In the tumor context, atonal acts by regulating cell proliferation and death via the JNK stress response pathway. Combined with evidence that atonal's mammalian homolog, ATOH1, is a tumor suppressor gene, our data support a critical, evolutionarily conserved, function for ato in oncogenesis.
- Published
- 2009
- Full Text
- View/download PDF
28. Integrating computational biology and forward genetics in Drosophila.
- Author
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Stein Aerts, Sven Vilain, Shu Hu, Leon-Charles Tranchevent, Roland Barriot, Jiekun Yan, Yves Moreau, Bassem A Hassan, and Xiao-Jiang Quan
- Subjects
Genetics ,QH426-470 - Abstract
Genetic screens are powerful methods for the discovery of gene-phenotype associations. However, a systems biology approach to genetics must leverage the massive amount of "omics" data to enhance the power and speed of functional gene discovery in vivo. Thus far, few computational methods for gene function prediction have been rigorously tested for their performance on a genome-wide scale in vivo. In this work, we demonstrate that integrating genome-wide computational gene prioritization with large-scale genetic screening is a powerful tool for functional gene discovery. To discover genes involved in neural development in Drosophila, we extend our strategy for the prioritization of human candidate disease genes to functional prioritization in Drosophila. We then integrate this prioritization strategy with a large-scale genetic screen for interactors of the proneural transcription factor Atonal using genomic deficiencies and mutant and RNAi collections. Using the prioritized genes validated in our genetic screen, we describe a novel genetic interaction network for Atonal. Lastly, we prioritize the whole Drosophila genome and identify candidate gene associations for ten receptor-signaling pathways. This novel database of prioritized pathway candidates, as well as a web application for functional prioritization in Drosophila, called Endeavour-HighFly, and the Atonal network, are publicly available resources. A systems genetics approach that combines the power of computational predictions with in vivo genetic screens strongly enhances the process of gene function and gene-gene association discovery.
- Published
- 2009
- Full Text
- View/download PDF
29. Fine-tuning enhancer models to predict transcriptional targets across multiple genomes.
- Author
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Stein Aerts, Jacques van Helden, Olivier Sand, and Bassem A Hassan
- Subjects
Medicine ,Science - Abstract
Networks of regulatory relations between transcription factors (TF) and their target genes (TG)- implemented through TF binding sites (TFBS)- are key features of biology. An idealized approach to solving such networks consists of starting from a consensus TFBS or a position weight matrix (PWM) to generate a high accuracy list of candidate TGs for biological validation. Developing and evaluating such approaches remains a formidable challenge in regulatory bioinformatics. We perform a benchmark study on 34 Drosophila TFs to assess existing TFBS and cis-regulatory module (CRM) detection methods, with a strong focus on the use of multiple genomes. Particularly, for CRM-modelling we investigate the addition of orthologous sites to a known PWM to construct phyloPWMs and we assess the added value of phylogenentic footprinting to predict contextual motifs around known TFBSs. For CRM-prediction, we compare motif conservation with network-level conservation approaches across multiple genomes. Choosing the optimal training and scoring strategies strongly enhances the performance of TG prediction for more than half of the tested TFs. Finally, we analyse a 35(th) TF, namely Eyeless, and find a significant overlap between predicted TGs and candidate TGs identified by microarray expression studies. In summary we identify several ways to optimize TF-specific TG predictions, some of which can be applied to all TFs, and others that can be applied only to particular TFs. The ability to model known TF-TG relations, together with the use of multiple genomes, results in a significant step forward in solving the architecture of gene regulatory networks.
- Published
- 2007
- Full Text
- View/download PDF
30. Emerging questions in transcriptional regulation
- Author
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Elphège P. Nora, Stein Aerts, Patricia J. Wittkopp, Harmen J. Bussemaker, Martha Bulyk, Saurabh Sinha, Julia Zeitlinger, Justin Crocker, and Juan Ignacio Fuxman Bass
- Subjects
Histology ,Cell Biology ,Pathology and Forensic Medicine - Published
- 2023
31. GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks.
- Author
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Thomas Moerman, Sara Aibar Santos, Carmen Bravo González-Blas, Jaak Simm, Yves Moreau, Jan Aerts, and Stein Aerts
- Published
- 2019
- Full Text
- View/download PDF
32. How regulatory sequences learn cell representations
- Author
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Stein Aerts
- Subjects
Learning ,Neural Networks, Computer ,Cell Biology ,Molecular Biology ,Biochemistry ,Biotechnology - Published
- 2022
33. Enhancer grammar of liver cell types and hepatocyte zonation states
- Author
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Carmen Bravo González-Blas, Irina Matetovici, Hanne Hillen, Ibrahim Ihsan Taskiran, Roel Vandepoel, Valerie Christiaens, Leticia Sansores-García, Elisabeth Verboven, Gert Hulselmans, Suresh Poovathingal, Jonas Demeulemeester, Nikoleta Psatha, David Mauduit, Georg Halder, and Stein Aerts
- Abstract
Cell type identity is encoded by gene regulatory networks (GRN), in which transcription factors (TFs) bind to enhancers to regulate target gene expression. In the mammalian liver, lineage TFs have been characterized for the main cell types, including hepatocytes. Hepatocytes cover a relatively broad cellular state space, as they differ significantly in their metabolic state, and function, depending on their position with respect to the central or portal vein in a liver lobule. It is unclear whether this spatially defined cellular state space, called zonation, is also governed by a well-defined gene regulatory code. To address this challenge, we have mapped enhancer-GRNs across liver cell types at high resolution, using a combination of single cell multiomics, spatial omics, GRN inference, and deep learning. We found that cell state changes in transcription and chromatin accessibility in hepatocytes, liver sinusoidal endothelial cells and hepatic stellate cells depend on zonation. Enhancer-GRN mapping suggests that zonation states in hepatocytes are driven by the repressors Tcf7l1 and Tbx3, that modulate the core hepatocyte GRN, controlled by Hnf4a, Cebpa, Hnf1a, Onecut1 and Foxa1, among others. To investigate how these TFs cooperate with cell type TFs, we performed anin vivomassively parallel reporter assay on 12,000 hepatocyte enhancers and used these data to train a hierarchical deep learning model (called DeepLiver) that exploits both enhancer accessibility and activity. DeepLiver confirms Cebpa, Onecut, Foxa1, Hnf1a and Hnf4a as drivers of enhancer specificity in hepatocytes; Tcf7l1/2 and Tbx3 as regulators of the zonation state; and Hnf4a, Hnf1a, AP-1 and Ets as activators. Finally, taking advantage ofin silicomutagenesis predictions from DeepLiver and enhancer assays, we confirmed that the destruction of Tcf7l1/2 or Tbx3 motifs in zonated enhancers abrogates their zonation bias. Our study provides a multi-modal understanding of the regulatory code underlying hepatocyte identity and their zonation state, that can be exploited to engineer enhancers with specific activity levels and zonation patterns.
- Published
- 2022
34. i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.
- Author
-
Hana Imrichová, Gert Hulselmans, Zeynep Kalender Atak, Delphine Potier, and Stein Aerts
- Published
- 2015
- Full Text
- View/download PDF
35. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
- Author
-
Carmen Bravo González-Blas, Seppe De Winter, Gert Hulselmans, Nikolai Hecker, Irina Matetovici, Valerie Christiaens, Suresh Poovathingal, Jasper Wouters, Sara Aibar, and Stein Aerts
- Abstract
Joint profiling of chromatin accessibility and gene expression of individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (eGRN). Here we present a new method for the inference of eGRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression. To improve both recall and precision of TF identification, we curated and clustered more than 40,000 position weight matrices that we could associate with 1,553 human TFs. We validated and benchmarked each of the SCENIC+ components on diverse data sets from different species, including human peripheral blood mononuclear cell types, ENCODE cell lines, human melanoma cell states, and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers, and GRNs between human and mouse cell types in the cerebral cortex. Finally, we provide new capabilities that exploit the inferred eGRNs to study the dynamics of gene regulation along differentiation trajectories; to map regulatory activities onto tissues using spatial omics data; and to predict the effect of TF perturbations on cell state. SCENIC+ provides critical insight into gene regulation, starting from multiome atlases of scATAC-seq and scRNA-seq. The SCENIC+ suite is available as a set of Python modules at https://scenicplus.readthedocs.io.
- Published
- 2022
36. Neuronal identity defines α-synuclein and tau toxicity
- Author
-
Roman Praschberger, Sabine Kuenen, Nils Schoovaerts, Natalie Kaempf, Jeevanjot Singh, Jasper Janssens, Jef Swerts, Eliana Nachman, Carles Calatayud, Stein Aerts, Suresh Poovathingal, and Patrik Verstreken
- Subjects
General Neuroscience - Published
- 2023
37. Neuronal identity defines α-synuclein and tau toxicity
- Author
-
Roman Praschberger, Sabine Kuenen, Nils Schoovaerts, Natalie Kaempf, Jasper Janssens, Jef Swerts, Eliana Nachman, Carles Calatayud, Stein Aerts, Suresh Poovathingal, and Patrik Verstreken
- Abstract
Pathogenic α-synuclein and tau are critical drivers of neurodegeneration and their mutations cause neuronal loss in patients. Whether the underlying preferential neuronal vulnerability is a cell-type intrinsic property or a consequence of increased expression levels is an open question. Here, we explore cell-type specific α-synuclein and tau expression in human brain datasets and use deep phenotyping as well as brain-wide single-cell RNA sequencing of >200 live neuron types in fruit flies to ask which cellular environments react most to α-synuclein or tau toxicity. We detect phenotypic and transcriptomic evidence of differential neuronal vulnerability independent of α-synuclein or tau expression levels. Comparing vulnerable with resilient neurons enabled us to identify molecular signatures associated with these differential responses. We used these to verify, and then predict resilient and vulnerable neuron subtypes in human brains. This confirms substantia nigra dopaminergic neurons to be sensitive to α-synuclein, and we predict pathogenic tau vulnerable and protected cortical neuron subtypes. Our work indicates that cellular determinants confer selective vulnerability to specific types of amyloid toxicity, thus paving the way to leverage neuronal identity to uncover modifiers of neurodegeneration-associated toxic proteins.
- Published
- 2022
38. Shared enhancer gene regulatory networks between wound and oncogenic programs
- Author
-
Swann Floc’hlay, Ramya Balaji, Valerie Christiaens, Carmen Bravo González-Blas, Seppe De Winter, Gert Hulselmans, Maxime De Waegeneer, Xiaojiang Quan, Duygu Koldere, Mardelle Atkins, Georg Halder, Anne Classen, and Stein Aerts
- Abstract
Wound response programs are often activated during neoplastic growth in tumors. In both wound repair and tumor growth, cells respond to acute stress and balance the activation of multiple programs including apoptosis, proliferation, and cell migration. Central to those responses are the activation of the JNK/MAPK and JAK/STAT signaling pathways. Yet, to what extent these signaling cascades interact at the cis-regulatory level, and how they orchestrate different regulatory and phenotypic responses is still unclear. Here, we aim to characterize the regulatory states that emerge and cooperate in the wound response, using the Drosophila melanogaster wing disc as a model system, and compare these with cancer cell states induced by rasV12scrib-/- in the eye disc. We used single-cell multiome profiling to derive enhancer Gene Regulatory Networks (eGRNs) by integrating chromatin accessibility and gene expression signals. We identify a “proliferative” eGRN, active in the majority of wounded cells and controlled by AP-1 and STAT. In a smaller, but distinct population of wound cells, a “senescent” eGRN is activated and driven by C/EBP-like transcription factors (Irbp18, Xrp1, Slow border, and Vrille) and Scalloped. In tumor cells on the other hand, both eGRN signatures are simultaneously active within the same cell. Our single-cell multiome and eGRNs resource offers an in-depth characterisation of the senescence markers, together with a new perspective on the shared gene regulatory programs acting during wound response and oncogenesis.
- Published
- 2022
39. Computational detection of cis-regulatory modules.
- Author
-
Stein Aerts, Peter Van Loo, Gert Thijs, Yves Moreau, and Bart De Moor
- Published
- 2003
40. Web-based Data Collection for Uterine Adnexal Tumors: A Case Study.
- Author
-
Stein Aerts, Peter Antal, Dirk Timmerman, Bart De Moor, and Yves Moreau
- Published
- 2002
- Full Text
- View/download PDF
41. Author response: Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads
- Author
-
Florian V De Rop, Joy N Ismail, Carmen Bravo González-Blas, Gert J Hulselmans, Christopher Campbell Flerin, Jasper Janssens, Koen Theunis, Valerie M Christiaens, Jasper Wouters, Gabriele Marcassa, Joris de Wit, Suresh Poovathingal, and Stein Aerts
- Published
- 2022
42. HyDrop-ATAC v1.0 v3
- Author
-
Florian De Rop, Suresh Poovathingal, and Stein Aerts
- Abstract
Step-by-step protocol for execution of HyDrop-ATAC.
- Published
- 2022
43. HyDrop-RNA v1.0 v2
- Author
-
Florian De Rop, Suresh Poovathingal, and Stein Aerts
- Abstract
Step-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.
- Published
- 2022
44. Microfluidic Chip Production v1.1 v3
- Author
-
Florian De Rop, Stein Aerts, and Suresh Poovathingal
- Abstract
Protocol for producing microfluidic chips used in HyDrop experiment.
- Published
- 2022
45. Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma
- Author
-
David Mauduit, Maxime de Waegeneer, Florian Rambow, Dennis Pedri, Jean-Christophe Marine, Samira Makhzami, Carmen Bravo González-Blas, Zeynep Kalender-Atak, Kristofer Davie, Stein Aerts, Ghanem Elias Ghanem, Ahmad Najem, Suresh Poovathingal, Michael Dewaele, Valerie Christiaens, Liesbeth Minnoye, Jasper Wouters, Gert Hulselmans, Frederik Ceyssens, and Katina I. Spanier
- Subjects
Transcription, Genetic ,MIGRATION ,INVASION ,SOX10 ,Gene regulatory network ,Computational biology ,Biology ,ACTIVATION ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Cell Movement ,Cell Line, Tumor ,Gene expression ,Humans ,Gene Regulatory Networks ,RNA, Neoplasm ,RNA-Seq ,TRANSCRIPTION FACTOR ,Melanoma ,Transcription factor ,SIGNATURES ,030304 developmental biology ,0303 health sciences ,Gene knockdown ,Science & Technology ,IDENTIFICATION ,SOXE Transcription Factors ,REPRESSOR ,PROFILES ,Cell Biology ,Phenotype ,Chromatin ,Cell biology ,Gene Expression Regulation, Neoplastic ,DIFFERENTIATION ,030220 oncology & carcinogenesis ,Life Sciences & Biomedicine ,STEM-CELLS ,Transcription Factors - Abstract
Melanoma cells can switch between a melanocytic and a mesenchymal-like state. Scattered evidence indicates that additional intermediate state(s) may exist. Here, to search for such states and decipher their underlying gene regulatory network (GRN), we studied 10 melanoma cultures using single-cell RNA sequencing (RNA-seq) as well as 26 additional cultures using bulk RNA-seq. Although each culture exhibited a unique transcriptome, we identified shared GRNs that underlie the extreme melanocytic and mesenchymal states and the intermediate state. This intermediate state is corroborated by a distinct chromatin landscape and is governed by the transcription factors SOX6, NFATC2, EGR3, ELF1 and ETV4. Single-cell migration assays confirmed the intermediate migratory phenotype of this state. Using time-series sampling of single cells after knockdown of SOX10, we unravelled the sequential and recurrent arrangement of GRNs during phenotype switching. Taken together, these analyses indicate that an intermediate state exists and is driven by a distinct and stable 'mixed' GRN rather than being a symbiotic heterogeneous mix of cells. ispartof: NATURE CELL BIOLOGY vol:22 issue:8 pages:986-+ ispartof: location:England status: published
- Published
- 2020
46. Decoding gene regulation in the fly brain
- Author
-
Jasper Janssens, Sara Aibar, Ibrahim Ihsan Taskiran, Joy N. Ismail, Alicia Estacio Gomez, Gabriel Aughey, Katina I. Spanier, Florian V. De Rop, Carmen Bravo González-Blas, Marc Dionne, Krista Grimes, Xiao Jiang Quan, Dafni Papasokrati, Gert Hulselmans, Samira Makhzami, Maxime De Waegeneer, Valerie Christiaens, Tony Southall, and Stein Aerts
- Subjects
CHROMATIN ,EXPRESSION ,DYNAMICS ,Multidisciplinary ,Science & Technology ,Brain ,Gene Expression Regulation, Developmental ,MOUSE ,SUBTYPES ,Multidisciplinary Sciences ,DROSOPHILA ,Gene Expression Regulation ,RESOURCE ,BINDING ,Animals ,Science & Technology - Other Topics ,RNA ,Drosophila ,Gene Regulatory Networks ,Transcription Factors - Abstract
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome analysis1-6, three-dimensional morphological classification7 and electron microscopy mapping of the connectome8,9 have revealed an immense diversity of neuronal and glial cell types that underlie an array of functional and behavioural traits in the fly. The identities of these cell types are controlled by gene regulatory networks (GRNs), involving combinations of transcription factors that bind to genomic enhancers to regulate their target genes. Here, to characterize GRNs at the cell-type level in the fly brain, we profiled the chromatin accessibility of 240,919 single cells spanning 9 developmental timepoints and integrated these data with single-cell transcriptomes. We identify more than 95,000 regulatory regions that are used in different neuronal cell types, of which 70,000 are linked to developmental trajectories involving neurogenesis, reprogramming and maturation. For 40 cell types, uniquely accessible regions were associated with their expressed transcription factors and downstream target genes through a combination of motif discovery, network inference and deep learning, creating enhancer GRNs. The enhancer architectures revealed by DeepFlyBrain lead to a better understanding of neuronal regulatory diversity and can be used to design genetic driver lines for cell types at specific timepoints, facilitating their characterization and manipulation. ispartof: NATURE vol:601 issue:7894 pages:630-+ ispartof: location:England status: published
- Published
- 2022
47. HyDrop Bead Generation & PCR Barcoding v1.0 v9
- Author
-
Florian De Rop, Suresh Poovathingal, and Stein Aerts
- Abstract
Protocol for producing dissolvable barcoded hydrogel beads used in HyDrop experiments.
- Published
- 2022
48. ENDEAVOUR update: a web resource for gene prioritization in multiple species.
- Author
-
Léon-Charles Tranchevent, Roland Barriot, Shi Yu, Steven Van Vooren, Peter Van Loo, Bert Coessens, Bart De Moor, Stein Aerts, and Yves Moreau
- Published
- 2008
- Full Text
- View/download PDF
49. ORegAnno: an open-access community-driven resource for regulatory annotation.
- Author
-
Obi L. Griffith, Stephen B. Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter J. De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth W. Wasserman, Ross C. Hardison, Casey M. Bergman, and Steven J. M. Jones
- Published
- 2008
- Full Text
- View/download PDF
50. Species-specific mitochondria dynamics and metabolism regulate the timing of neuronal development
- Author
-
Ryohei Iwata, Pierre Casimir, Emir Erkol, Leïla Boubakar, Mélanie Planque, Martyna Ditkowska, Katlijn Vints, Suresh Poovathingal, Vaiva Gaspariunaite, Matthew Bird, Nikky Corthout, Pieter Vermeersch, Kristofer Davie, Natalia V. Gounko, Stein Aerts, Bart Ghesquière, Sarah-Maria Fendt, and Pierre Vanderhaeghen
- Abstract
The evolution of species involves changes in the timeline of key developmental programs. Among these, neuronal development is considerably prolonged in the human cerebral cortex compared with other mammals, leading to brain neoteny. Here we explore whether mitochondria influence the species-specific properties of cortical neuron maturation. By comparing human and mouse cortical neuronal maturation at high temporal and cell resolution, we found a slower pattern of mitochondria development in human cortical neurons compared with the mouse, together with lower mitochondria metabolic activity, particularly oxidative phosphorylation. Stimulation of mitochondria metabolism in human neurons resulted in accelerated maturation, leading to excitable and complex cells weeks ahead of time. Our data identify mitochondria as important regulators of the pace of neuronal development underlying human-specific features of brain evolution.
- Published
- 2021
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